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• waveOrder v2 milestones

  Release 2.0.0 ------------- 1. New memory-efficient wave optical models and inverse algorithms for single-photon scalar imaging, i.e., absorption, phase, and fluorescence. These models are compatible with multiprocessing and distributed computing workflows. 2. Similar implementations of geometrical models and inverse algorithms for single-photon vector imaging, i.e., label-free imaging of retardance and orientation; and fluorescence imaging of dipole anisotropy and orientation. 3. Initial refactor of wave optical models and inverse algorithms for single-photon vector imaging, i.e., permittivity tensor imaging and joint deconvolution of phase and retardance. (1) and (2) will be implemented with pytorch API to enable GPU-accelerated analysis across platforms. The use of pytorch will enable data-driven optimization of parameters of the inverse algorithms and online reconstruction. (3) will initially use a mix of numpy, cupy, and pytorch. Release 2.1.0 ----------- 1. Python script and PDF that illustrates PTI reconstruction. Release 2.2.0 ------------- 1. Reimplement phase reconstruction algorithms to measure the density of tissues such as zebrafish. 2. Calibrating the optical transfer functions (OTFs) from acquired beads data or Fourier ring correlation for deconvolution of phase, widefield fluorescence, and light-sheet datasets. 3. Forward model and inverse algorithm for joint deconvolution of phase, retardance, and orientation implemented in pytorch and compatible with parallel execution. These algorithms will be tested with a variety of existing datasets, particularly zebrafish.

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